My interpretation is that his healing factor wasn't gone completely just slowed/neutered a bit. Considering the hits he took his healing factor had to somewhat still be there because he still took some pretty serious wounds. It's possible is knuckles had enough "healing memory" to do that process quickly.
The other answer I have is.... LOOK! Is that a flying kitten?!
That's the conclusion I came to as well, after all, if his healing factor was gone completely then he would have been done in by adamantium poisoning.